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1 | (4) |
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2 Review of Organic Chemistry |
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5 | (22) |
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2.1 Electrovalent and Covalent Bonds |
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6 | (3) |
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2.2 Some Chemical Bonds and Groups Commonly Encountered in Biological Molecules |
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9 | (4) |
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2.3 Building Blocks for Common Organic Molecules |
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13 | (14) |
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13 | (4) |
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17 | (1) |
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18 | (2) |
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20 | (7) |
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3 Energy Considerations in Biochemical Reactions |
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27 | (10) |
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3.1 Some Common Biochemical Reactions |
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28 | (2) |
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28 | (1) |
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3.1.2 Cellular Respiration |
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29 | (1) |
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3.1.3 Oxidation and Reduction |
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29 | (1) |
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30 | (2) |
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3.3 Feasibility of Chemical Reactions |
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32 | (2) |
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3.4 Activated Carrier Molecules and Their Role in Biosynthesis |
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34 | (3) |
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37 | (16) |
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4.1 Protein Structure and Function |
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37 | (4) |
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4.1.1 The a-helix and the 0-sheet |
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38 | (3) |
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4.2 Levels of Organization in Proteins |
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41 | (2) |
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4.3 Protein Ligand Interactions |
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43 | (2) |
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4.4 Isolating Proteins from Cells |
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45 | (1) |
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4.5 Separating a Mixture of Proteins |
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46 | (2) |
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4.5.1 Column Chromatography |
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47 | (1) |
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4.5.2 Gel Electrophoresis |
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47 | (1) |
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4.6 Protein Structure Determination |
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48 | (1) |
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4.7 Proteins That Are Enzymes |
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49 | (4) |
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53 | (10) |
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6 Transcription and Translation |
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63 | (14) |
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64 | (5) |
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69 | (8) |
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7 Chromosomes and Gene Regulation |
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77 | (12) |
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7.1 Organization of DNA into Chromosomes |
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78 | (4) |
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82 | (7) |
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89 | (12) |
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8.1 Genetic Variation in Bacteria |
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89 | (5) |
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90 | (2) |
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8.1.2 Gene Transfer by Bacteriophages |
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92 | (1) |
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93 | (1) |
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8.2 Sources of Genetic Change in Eucaryotic Genomes |
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94 | (7) |
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94 | (2) |
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8.2.2 Transposable Elements and Viruses |
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96 | (2) |
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8.2.3 Sexual Reproduction and the Reassortment of Genes |
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98 | (3) |
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101 | (16) |
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9.1 Techniques for Analyzing DNA Molecules |
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101 | (4) |
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9.2 Nucleic Acid Hybridization and Associated Techniques |
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105 | (2) |
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9.3 Construction of Human Genomic and cDNA Libraries |
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107 | (2) |
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9.4 Polymerase Chain Reaction (PCR) |
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109 | (3) |
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112 | (7) |
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9.5.1 Engineering DNA Molecules, Proteins and RNAs |
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112 | (1) |
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9.5.2 Engineering Mutant Haploid Organisms |
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112 | (2) |
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9.5.3 Engineering Transgenic Animals |
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114 | (3) |
10 Cell Division |
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117 | (10) |
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10.1 Mitosis and Cytokinesis |
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119 | (4) |
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123 | (4) |
11 Cell Cycle Control, Cell Death and Cancer |
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127 | (10) |
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11.1 Cyclin-Dependent Kinases and Their Role |
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128 | (3) |
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11.2 Control of Cell Numbers in Multicellular Organisms |
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131 | (1) |
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11.3 Programmed Cell Death |
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132 | (1) |
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11.4 Cancer as the Breakdown of Cell Cycle Control |
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133 | (4) |
12 Expression Microarrays |
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137 | (10) |
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138 | (7) |
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140 | (2) |
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142 | (3) |
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12.2 Synthetic Oligonucleotide Arrays |
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145 | (2) |
13 Classification |
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147 | (20) |
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147 | (11) |
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148 | (1) |
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13.1.2 Classification Rules |
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148 | (3) |
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13.1.3 Constrained Classifier Design |
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151 | (3) |
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13.1.4 Regularization for Quadratic Discriminant Analysis |
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154 | (3) |
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13.1.5 Regularization by Noise Injection |
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157 | (1) |
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158 | (3) |
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161 | (7) |
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13.3.1 Error Estimation Using the Training Data |
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162 | (1) |
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13.3.2 Performance Issues |
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163 | (4) |
14 Clustering |
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167 | (14) |
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14.1 Examples of Clustering Algorithms |
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168 | (5) |
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168 | (1) |
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169 | (1) |
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14.1.3 Self-Organizing Maps |
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170 | (1) |
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14.1.4 Hierarchical Clustering |
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171 | (2) |
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173 | (3) |
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14.2.1 Model-Based Clustering Error |
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173 | (1) |
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14.2.2 Application to Real Data |
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174 | (2) |
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176 | (5) |
15 Genetic Regulatory Networks |
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181 | (16) |
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15.1 Nonlinear Dynamical Modeling of Gene Networks |
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182 | (2) |
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184 | (4) |
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184 | (3) |
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15.2.2 Coefficient of Determination |
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187 | (1) |
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15.3 Probabilistic Boolean Networks |
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188 | (4) |
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192 | (5) |
16 Intervention |
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197 | (10) |
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198 | (1) |
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16.2 Intervention by Flipping the Status of a Single Gene |
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199 | (4) |
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16.3 Intervention to Alter the Steady-State Behavior |
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203 | (4) |
17 External Intervention Based on Optimal Control Theory |
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207 | (46) |
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17.1 Finite-Horizon-Control |
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208 | (12) |
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17.1.1 Solution Using Dynamic Programming |
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211 | (1) |
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17.1.2 A Simple Illustrative Example |
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212 | (3) |
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215 | (5) |
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17.2 External Intervention in the Imperfect Information Case |
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220 | (6) |
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221 | (5) |
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17.3 External Intervention in the Context-Sensitive Case |
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226 | (6) |
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229 | (3) |
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17.4 External Intervention for a Family of Boolean Networks |
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232 | (6) |
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235 | (3) |
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17.5 External Intervention in the Infinite Horizon Case |
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238 | (10) |
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17.5.1 Optimal Control Solution |
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240 | (4) |
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244 | (4) |
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248 | (5) |
References |
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253 | (12) |
Index |
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265 | |